Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 4M75
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.2 14.4 - - + -
54A ILE* 4.8 1.8 - - + -
56A VAL* 4.7 11.9 - - + -
68A LEU* 3.8 18.4 - - + -
70A THR 3.6 2.5 - - - -
71A PHE* 3.6 23.8 - - + -
75A ALA* 3.4 20.4 - - - +
76A ASN* 1.3 72.8 - - - +
78A ILE* 1.3 62.9 + - - +
79A LEU* 4.1 15.9 - - + -
102A PHE 3.9 0.2 - - - +
103A MSE 3.3 6.7 - - - +
104A ILE* 2.7 41.5 + - + +
109A VAL* 4.5 15.9 - - + -
112A LEU* 4.2 23.3 - - + -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.3 6.2 - - - +
69A ARG* 2.9 35.6 + - + -
70A THR* 2.9 33.6 + - + +
77A LEU* 1.3 76.5 - - - +
79A LEU* 1.3 63.8 + - - +
101A ILE* 4.1 18.8 - - + -
102A PHE 3.5 7.0 - - - +
103A MSE 3.2 34.8 - - + -
3G PRO* 3.8 21.5 - - + +
6G LEU* 4.3 17.5 - - + -
7G LEU 5.8 0.2 - - - +
81G LEU* 4.7 5.2 - - + -
86G ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.0 12.6 - - + -
56A VAL* 4.2 19.3 - - + -
64A LEU* 4.9 1.8 - - + -
65A PHE 4.2 1.6 - - - -
66A GLY* 4.1 23.3 - - - +
67A VAL 3.5 10.3 - - - +
68A LEU* 3.7 17.0 - - + -
69A ARG 5.3 0.2 - - - -
77A LEU* 4.1 14.8 - - + -
78A ILE* 1.3 82.6 - - - +
80A GLN* 1.3 61.1 + - - +
82A CYS* 3.8 30.5 - - + -
100A GLY 3.8 0.6 - - - +
101A ILE* 3.3 11.5 - - - +
102A PHE* 3.0 31.9 + - + +
104A ILE* 4.7 11.7 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY* 3.8 0.5 - - - -
67A VAL* 2.9 28.1 + - + +
69A ARG* 2.1 61.5 + - + +
78A ILE 4.4 0.2 + - - -
79A LEU* 1.3 74.0 - - - +
81A ASP* 1.3 82.2 + - + +
82A CYS 3.1 1.6 + - - -
100A GLY 4.1 1.3 - - - -
101A ILE* 4.3 19.6 - - + +
86G ILE* 4.3 23.4 - - + +
87G ASP* 5.5 2.6 + - - -
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 5.9 0.3 + - - -
65A PHE 3.8 4.3 - - - +
66A GLY* 3.9 4.6 - - - -
67A VAL* 5.1 7.2 - - + +
80A GLN* 1.3 85.8 + - + +
82A CYS* 1.3 65.7 + - - +
83A VAL* 3.6 10.5 + - - +
100A GLY* 3.2 11.2 + - - -
101A ILE* 4.7 1.2 - - - +
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Residues in contact with CYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.4 38.6 - - - -
65A PHE 3.2 10.5 - - - -
66A GLY* 4.4 0.4 - - - -
79A LEU* 3.8 23.6 - - + -
80A GLN 3.1 2.4 - - - -
81A ASP* 1.3 74.6 - - - +
83A VAL* 1.3 60.3 + - - +
98A ASP* 4.0 0.5 - - - +
99A ARG* 2.6 40.7 + - + -
100A GLY 2.5 27.7 + - - +
102A PHE* 4.4 12.8 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 5.7 4.5 - - - +
64A LEU* 3.5 3.8 - - - -
65A PHE* 2.6 54.1 + - + +
81A ASP 4.0 9.0 - - - +
82A CYS* 1.3 81.2 - - - +
84A GLU* 1.3 66.2 + - - +
85A ARG* 3.9 3.0 + - + +
96A GLU* 3.3 35.0 - - + +
97A GLU 3.5 11.9 - - - +
98A ASP* 4.2 17.9 - - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.4 39.8 + - + +
63A MSE 3.5 12.1 - - - +
64A LEU* 3.7 14.8 - - + +
83A VAL* 1.3 74.4 - - - +
85A ARG* 1.3 63.3 + - - +
86A ILE* 4.2 7.4 - - + +
96A GLU* 3.5 3.6 - - - -
97A GLU 3.0 31.6 + - - +
99A ARG* 2.8 44.6 + - - +
102A PHE* 5.4 1.6 - - - -
132A PHE* 4.1 19.8 - - + -
136A TRP* 5.0 9.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il